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Vitrac H, Mallampalli VKPS, Bogdanov M, Dowhan W. The lipid-dependent structure and function of LacY can be recapitulated and analyzed in phospholipid-containing detergent micelles. Sci Rep 2019; 9:11338. [PMID: 31383935 PMCID: PMC6683142 DOI: 10.1038/s41598-019-47824-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/24/2019] [Indexed: 12/19/2022] Open
Abstract
Membrane proteins play key roles in cellular functions, their activity mainly depending on their topological arrangement in membranes. Structural studies of membrane proteins have long adopted a protein-centric view regarding the determinants of membrane protein topology and function. Several studies have shown that the orientation of transmembrane domains of polytopic membrane proteins with respect to the plane of the lipid bilayer can be largely determined by membrane lipid composition. However, the mechanism by which membrane proteins exhibit structural and functional duality in the same membrane or different membranes is still unknown. Here we show that lipid-dependent structural and functional assessment of a membrane protein can be conducted in detergent micelles, opening the possibility for the determination of lipid-dependent high-resolution crystal structures. We found that the lactose permease purified from Escherichia coli cells exhibiting varied phospholipid compositions exhibits the same topology and similar function as in its membrane of origin. Furthermore, we found several conditions, including protein mutations and micelle lipid composition, that lead to increased protein stability, correlating with a higher yield of two-dimensional crystal formation. Altogether, our results demonstrate how the membrane lipid environment influences membrane protein topology and arrangement, both in native membranes and in mixed detergent micelles.
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Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology and the Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA.
| | - Venkata K P S Mallampalli
- Department of Biochemistry and Molecular Biology and the Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology and the Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology and the Center for Membrane Biology, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA.
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2
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Padariya M, Kalathiya U, Baginski M. Structural and dynamic insights on the EmrE protein with TPP + and related substrates through molecular dynamics simulations. Chem Phys Lipids 2018; 212:1-11. [DOI: 10.1016/j.chemphyslip.2017.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022]
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Vitrac H, MacLean DM, Karlstaedt A, Taegtmeyer H, Jayaraman V, Bogdanov M, Dowhan W. Dynamic Lipid-dependent Modulation of Protein Topology by Post-translational Phosphorylation. J Biol Chem 2016; 292:1613-1624. [PMID: 27974465 DOI: 10.1074/jbc.m116.765719] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/13/2016] [Indexed: 01/01/2023] Open
Abstract
Membrane protein topology and folding are governed by structural principles and topogenic signals that are recognized and decoded by the protein insertion and translocation machineries at the time of initial membrane insertion and folding. We previously demonstrated that the lipid environment is also a determinant of initial protein topology, which is dynamically responsive to post-assembly changes in membrane lipid composition. However, the effect on protein topology of post-assembly phosphorylation of amino acids localized within initially cytoplasmically oriented extramembrane domains has never been investigated. Here, we show in a controlled in vitro system that phosphorylation of a membrane protein can trigger a change in topological arrangement. The rate of change occurred on a scale of seconds, comparable with the rates observed upon changes in the protein lipid environment. The rate and extent of topological rearrangement were dependent on the charges of extramembrane domains and the lipid bilayer surface. Using model membranes mimicking the lipid compositions of eukaryotic organelles, we determined that anionic lipids, cholesterol, sphingomyelin, and membrane fluidity play critical roles in these processes. Our results demonstrate how post-translational modifications may influence membrane protein topology in a lipid-dependent manner, both along the organelle trafficking pathway and at their final destination. The results provide further evidence that membrane protein topology is dynamic, integrating for the first time the effect of changes in lipid composition and regulators of cellular processes. The discovery of a new topology regulatory mechanism opens additional avenues for understanding unexplored structure-function relationships and the development of optimized topology prediction tools.
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Affiliation(s)
- Heidi Vitrac
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
| | - David M MacLean
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Anja Karlstaedt
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Heinrich Taegtmeyer
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Vasanthi Jayaraman
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Mikhail Bogdanov
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - William Dowhan
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
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4
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LeBarron J, London E. Effect of lipid composition and amino acid sequence upon transmembrane peptide-accelerated lipid transleaflet diffusion (flip-flop). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1812-20. [PMID: 27131444 DOI: 10.1016/j.bbamem.2016.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/21/2016] [Accepted: 04/21/2016] [Indexed: 12/15/2022]
Abstract
We examined how hydrophobic peptide-accelerated transleaflet lipid movement (flip-flop) was affected by peptide sequence and vesicle composition and properties. A peptide with a completely hydrophobic sequence had little if any effect upon flip-flop. While peptides with a somewhat less hydrophobic sequence accelerated flip-flop, the half-time remained slow (hours) with substantial (0.5mol%) peptide in the membranes. It appears that peptide-accelerated lipid flip-flop involves a rare event that may reflect a rare state of the peptide or lipid bilayer. There was no simple relationship between peptide overall hydrophobicity and flip-flop. In addition, flip-flop was not closely linked to whether the peptides were in a transmembrane or non-transmembrane (interfacial) inserted state. Flip-flop was also not associated with peptide-induced pore formation. We found that peptide-accelerated flip-flop is initially faster in small (highly curved) unilamellar vesicles relative to that in large unilamellar vesicles. Peptide-accelerated flip-flop was also affected by lipid composition, being slowed in vesicles with thick bilayers or those containing 30% cholesterol. Interestingly, these factors also slow spontaneous lipid flip-flop in the absence of peptide. Combined with previous studies, the results are most consistent with acceleration of lipid flip-flop by peptide-induced thinning of bilayer width.
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Affiliation(s)
- Jamie LeBarron
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
| | - Erwin London
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
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5
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Bellmann-Sickert K, Stone TA, Poulsen BE, Deber CM. Efflux by small multidrug resistance proteins is inhibited by membrane-interactive helix-stapled peptides. J Biol Chem 2014; 290:1752-9. [PMID: 25425644 DOI: 10.1074/jbc.m114.616185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacterial cell membranes contain several protein pumps that resist the toxic effects of drugs by efficiently extruding them. One family of these pumps, the small multidrug resistance proteins (SMRs), consists of proteins of about 110 residues that need to oligomerize to form a structural pathway for substrate extrusion. As such, SMR oligomerization sites should constitute viable targets for efflux inhibition, by disrupting protein-protein interactions between helical segments. To explore this proposition, we are using Hsmr, an SMR from Halobacter salinarum that dimerizes to extrude toxicants. Our previous work established that (i) Hsmr dimerization is mediated by a helix-helix interface in Hsmr transmembrane (TM) helix 4 (residues (90)GLALIVAGV(98)); and (ii) a peptide comprised of the full TM4(85-105) sequence inhibits Hsmr-mediated ethidium bromide efflux from bacterial cells. Here we define the minimal linear sequence for inhibitor activity (determined as TM4(88-100), and then "staple" this sequence via Grubbs metathesis to produce peptides typified by acetyl-A-(Sar)3-(88)VVGLXLIZXGVVV(100)-KKK-NH2 (X = 2-(4'-pentenyl)alanine at positions 92 and 96; Z = Val, Gly, or Asn at position 95)). The Asn(95) peptide displayed specific efflux inhibition and resensitization of Hsmr-expressing cells to ethidium bromide; and was non-hemolytic to human red blood cells. Stapling essentially prevented peptide degradation in blood plasma and liver homogenates versus an unstapled counterpart. The overall results confirm that the stapled analog of TM4(88-100) retains the structural complementarity required to disrupt the Hsmr TM4-TM4 locus in Hsmr, and portend the general validity of stapled peptides as therapeutics for the disruption of functional protein-protein interactions in membranes.
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Affiliation(s)
- Kathrin Bellmann-Sickert
- From the Division of Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and
| | - Tracy A Stone
- From the Division of Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Bradley E Poulsen
- From the Division of Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Charles M Deber
- From the Division of Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4 and the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Banigan JR, Gayen A, Cho MK, Traaseth NJ. A structured loop modulates coupling between the substrate-binding and dimerization domains in the multidrug resistance transporter EmrE. J Biol Chem 2014; 290:805-14. [PMID: 25406320 DOI: 10.1074/jbc.m114.601963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Secondary active transporters undergo large conformational changes to facilitate the efflux of substrates across the lipid bilayer. Among the smallest known transport proteins are members of the small multidrug resistance (SMR) family that are composed of four transmembrane (TM) domains and assemble into dimers. An unanswered question in the SMR field is how the dimerization domain (TM4) is coupled with the substrate-binding chamber (TM1-3). To provide insight for this essential aspect of ion-coupled transport, we carried out a structure-function study on the SMR protein EmrE using solid-state NMR spectroscopy in lipid bilayers and resistance assays in Escherichia coli. The chemical shifts for EmrE were consistent with β-strand secondary structure for the loop connecting TM3 and TM4. Based on these structural results, EmrE mutants were created to ascertain whether a specific loop length and composition were necessary for function. A linker encompassing six extra Gly residues relative to wild-type EmrE failed to give resistance; however, the number of residues in the loop was not the only criterion for a functional efflux pump. Replacement of the central hydrophobic residue with Gly (L83G) also conferred no ethidium resistance phenotype, which supported the conclusion that the structure and length of the loop were both essential for ion-coupled transport. Taken together with a bioinformatics analysis, a structured linker is likely conserved across the SMR family to play an active role in mediating the conformational switch between inward-open and outward-open states necessary for drug efflux. These findings underscore the important role loops can play in mediating efflux.
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Affiliation(s)
- James R Banigan
- From the Department of Chemistry, New York University, New York, New York 10003
| | - Anindita Gayen
- From the Department of Chemistry, New York University, New York, New York 10003
| | - Min-Kyu Cho
- From the Department of Chemistry, New York University, New York, New York 10003
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Springer S, Malkus P, Borchert B, Wellbrock U, Duden R, Schekman R. Regulated Oligomerization Induces Uptake of a Membrane Protein into COPII Vesicles Independent of Its Cytosolic Tail. Traffic 2014; 15:531-45. [DOI: 10.1111/tra.12157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/07/2014] [Accepted: 01/30/2014] [Indexed: 12/22/2022]
Affiliation(s)
| | - Per Malkus
- Department of Systems Biology; Harvard Medical School; Boston MA 02115 USA
| | - Britta Borchert
- Biochemistry and Cell Biology; Jacobs University Bremen; Bremen Germany
| | - Ursula Wellbrock
- Biochemistry and Cell Biology; Jacobs University Bremen; Bremen Germany
| | - Rainer Duden
- Centre for Structural and Cell Biology in Medicine, Institute of Biology; University of Lübeck; Lübeck Germany
| | - Randy Schekman
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology; University of California, Berkeley; Berkeley CA 94720 USA
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Lloris-Garcerá P, Slusky JSG, Seppälä S, Prieß M, Schäfer LV, von Heijne G. In vivo trp scanning of the small multidrug resistance protein EmrE confirms 3D structure models'. J Mol Biol 2013; 425:4642-51. [PMID: 23920359 DOI: 10.1016/j.jmb.2013.07.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/10/2013] [Accepted: 07/28/2013] [Indexed: 11/28/2022]
Abstract
The quaternary structure of the homodimeric small multidrug resistance protein EmrE has been studied intensely over the past decade. Structural models derived from both two- and three-dimensional crystals show EmrE as an anti-parallel homodimer. However, the resolution of the structures is rather low and their relevance for the in vivo situation has been questioned. Here, we have challenged the available structural models by a comprehensive in vivo Trp scanning of all four transmembrane helices in EmrE. The results are in close agreement with the degree of lipid exposure of individual residues predicted from coarse-grained molecular dynamics simulations of the anti-parallel dimeric structure obtained by X-ray crystallography, strongly suggesting that the X-ray structure provides a good representation of the active in vivo form of EmrE.
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Affiliation(s)
- Pilar Lloris-Garcerá
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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